Variant report

Variant	rs7971877
Chromosome Location	chr12:58287630-58287631
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58236711..58242486-chr12:58286970..58293951,15	MCF-7	breast:
2	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTDSP2-1	chr12:58287523-58290265	ENSG00000245651
2	lnc-CTDSP2-1	chr12:58287523-58287735	ENSG00000245651
3	lnc-CTDSP2-1	chr12:58287523-58290267	XLOC_010101
4	lnc-CTDSP2-1	chr12:58287523-58290265	ENSG00000245651

No data

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10747786	0.83[CHD][hapmap]
rs10747787	0.83[CHD][hapmap]
rs10877029	0.83[CHD][hapmap]
rs10877030	0.83[CHD][hapmap]
rs10877033	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877034	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172367	0.80[CHD][hapmap]
rs11172371	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs11172372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172378	0.88[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs1962047	0.88[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs2002275	0.88[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs3751330	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751331	0.80[ASN][1000 genomes]
rs4128707	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4237844	0.81[CHD][hapmap]
rs4237845	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4417327	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4553410	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4630335	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs4760172	0.83[CHD][hapmap]
rs4760340	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.83[ASN][1000 genomes]
rs6581157	0.81[ASN][1000 genomes]
rs6650217	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6650218	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6650219	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312623	0.83[CHD][hapmap]
rs7954591	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7954957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963992	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7971877	XRCC6BP1	cis	Artery Tibial	GTEx
rs7971877	XRCC6BP1	cis	Nerve Tibial	GTEx
rs7971877	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs7971877	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7971877	NCKAP1L	cis	cerebellum	SCAN
rs7971877	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs7971877	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs7971877	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs7971877	XRCC6BP1	cis	lung	GTEx
rs7971877	XRCC6BP1	cis	Thyroid	GTEx
rs7971877	XRCC6BP1	cis	Whole Blood	GTEx
rs7971877	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs7971877	XRCC6BP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58280400-58288000	Enhancers	Fetal Intestine Large	intestine
2	chr12:58281000-58288000	Enhancers	Fetal Muscle Trunk	muscle
3	chr12:58281400-58287800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:58281400-58287800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:58281600-58288400	Enhancers	K562	blood
6	chr12:58282200-58289600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:58282400-58287800	Enhancers	Ovary	ovary
8	chr12:58283000-58287800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:58283000-58288200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:58283000-58288200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:58283200-58288400	Weak transcription	Primary T cells from cord blood	blood
12	chr12:58283200-58288400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:58283400-58288400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:58284400-58287800	Enhancers	Colonic Mucosa	Colon
15	chr12:58285000-58288000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:58285600-58287800	Enhancers	Fetal Heart	heart
17	chr12:58285600-58290000	Enhancers	Brain Angular Gyrus	brain
18	chr12:58285600-58290000	Enhancers	Left Ventricle	heart
19	chr12:58285600-58290200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr12:58285800-58289600	Enhancers	Duodenum Mucosa	Duodenum
21	chr12:58285800-58289800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr12:58285800-58290000	Enhancers	Placenta	Placenta
23	chr12:58285800-58290000	Enhancers	Right Atrium	heart
24	chr12:58285800-58290000	Enhancers	Right Ventricle	heart
25	chr12:58285800-58290200	Enhancers	Lung	lung
26	chr12:58286000-58287800	Enhancers	GM12878-XiMat	blood
27	chr12:58286000-58289800	Enhancers	Stomach Mucosa	stomach
28	chr12:58286000-58290600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:58286200-58289400	Enhancers	Brain Cingulate Gyrus	brain
30	chr12:58286200-58290000	Enhancers	Fetal Thymus	thymus
31	chr12:58286400-58288200	Weak transcription	Spleen	Spleen
32	chr12:58286400-58289800	Enhancers	Brain Substantia Nigra	brain
33	chr12:58286600-58288200	Weak transcription	Aorta	Aorta
34	chr12:58286600-58288400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr12:58286600-58288400	Weak transcription	Esophagus	oesophagus
36	chr12:58286600-58289600	Enhancers	Fetal Brain Female	brain
37	chr12:58286600-58290200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr12:58286800-58287800	Enhancers	Adipose Nuclei	Adipose
39	chr12:58286800-58289800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:58286800-58291400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:58287000-58288400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:58287000-58288400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:58287000-58288400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:58287000-58288400	Enhancers	A549	lung
45	chr12:58287000-58288600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr12:58287000-58288600	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr12:58287000-58289600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:58287000-58289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:58287000-58290000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:58287200-58287800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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